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We study the family of network models derived by requiring the expected properties of a graph ensemble to match a given set of measurements of a real-world network, while maximizing the entropy of the ensemble. Models of this type play the…
Formation of a molecular network from multifunctional precursors is modelled with a random graph process. The random graph model favours reactivity for monomers that are positioned close in the network topology, and disfavours reactivity…
Thermodynamic description of a model system with magnetoelastic coupling is presented. The elastic, vibrational, electronic and magnetic energy contributions are taken into account. The long-range RKKY interaction is considered together…
A recent article by Weidner et al. [2021] presents a method to extract graph properties that are predictive of the dynamical behavior of multivariate, discrete models of biochemical regulation. In other words, a method that uses only…
We study the structure of Fermionic networks, i.e., a model of networks based on the behavior of fermionic gases, and we analyze dynamical processes over them. In this model, particle dynamics have been mapped to the domain of networks,…
We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…
We present an exact derivation of the isobaric partition function of lattice hard rods with arbitrary nearest neighbor interactions. Free energy and all thermodynamics functions are derived accordingly and they written in a form that is a…
Network embedding is a fervid topic in current networks science and observes that most real complex systems can be embedded in hidden metrics space and emerge as the geometrical property, where the geometric distance between nodes…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
We show how arbitrary unit cells of periodic materials can be represented as graphs whose nodes represent atoms and whose weighted edges represent tunneling connections between atoms. Further, we present methods to calculate the band…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
The heterogeneity of breast cancer presents considerable challenges for its early detection, prognosis, and treatment selection. Convolutional neural networks often neglect the spatial relationships within histopathological images, which…
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprised of two…
Thermodynamics is accepted as a universal truth, encompassing all macroscopic objects. Therefore, it is surprising to find that, within our current understanding, the photovoltaic effect has so far eluded the first and second laws of…
We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…
Effective information analysis generally boils down to properly identifying the structure or geometry of the data, which is often represented by a graph. In some applications, this structure may be partly determined by design constraints or…
Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…